PART I

PART II

PART III

INTRO PAGE

LEMURS OF MADAGASCAR

PART II: COMMUNICATION SIGNALS

Click here to learn more about the Lemurs in this practical (Pictures and data by ETI. The descriptions of the species in the pop up window are actually 'IUCN redbook reports'. Note that these reports follow an old - and taxonomically speaking incorrect - nomenclature for the taxa. We'll see later on why the names are incorrect.)

This is the second part of the Lemur practical. In this part you'll learn to work with Paup and MacClade. It is essential that you have read the manuals (don't worry, they're only a couple of pages) and that you have them permanently at your disposal. To avoid screen clutter, you might want to print these manuals so that you have them available as hard copies. You'll find the manuals here (they come in the form of one MSWord document).

Type your answers in the text areas on this screen. Press the 'submit' button when you're done.

In this part of the practical we'll work on the communication signals of a number of Lemur species. As a first exercise your task is to listen to the sounds and look at the sonograms for a character defined in the literature as 'disturbance clicks and grunts'. This character has three states, so the clicks & grunts are classified as consisting of either (1) a single element; (2) two distinct elements; or (3) multiples of same element type.

  1. Assign the described character states to the taxa in the text box using the information you can gather from the sounds and sonograms in the pop up window.


  2. We're going to work on a real dataset, taken from Macedonia & Stanger (1994). Create a folder on your desktop and give it a useful name (e.g. 'matrices'). Download the file communicationsignals and save it in your matrices folder. Start PAUP and open the file 'communicationsignals'. The matrix is a 'NEXUS' files. This is not really a proprietary file format. Rather, these matrices are 'plain text' files (so you can also open and edit NEXUS files in SimpleText, or in your browser for instance) that follow a rather strict syntax. The 'clicks and grunts' character you've worked on was number 6. Compare the character states you've assigned to the states in the matrix.

    Take a look at the description of the characters and their respective states.

    Run a branch and bound search in Paup. Leave all characters unweighted and unordered.

    What's different about the nomenclature [the names of the Lemurs] used in this matrix compared to the redbook reports [the redbook reports are the species descriptions in the pop up window. Look for the names in italics. Do the trees justify this change?


  3. We’re looking at unrooted trees, and we haven’t defined any outgroups. When you answered the previous question, did you realise that it was an unrooted tree you’re looking at? Does it make a difference for your answer?


  4. Root the tree on Daubentonia. Investigation of skull forms and sizes has shown that Lemurand Eulemurskulls are almost identical, whereas Lemurand Hapalemurshow distinct differences. Is this what you would expect from the tree you have constructed?


  5. It has been proposed to rename Lemur catta Eulemur catta. Is that an obvious suggestion based on the data we have?


  6. How many changes would your tree have if every character were an unambiguous derived character state (synapomorphy) and the tree would not contain homoplasy (e.g. excess changes resulting from parallel or convergent evolutions and from character state reversals)? Hint: look at the character description table again.


  7. If the c.i. (consistency index) is simply (minimum length of a tree)/(actual length of a tree), then what is the c.i. for your tree?


  8. Save the tree and open the matrix and the tree in MacClade. Go to the tree window and reroot the tree on Daubentonia madagascariensis. Start the ‘trace character’ option.

    Which characters/states are derived character states (synapomorphies) for the Eulemurs?


  9. Which characters/states are derived character states (synapomorphies) for the Hapalemur/Lemur clade?


  10. Which characters show homoplasies?


  11. Consider character 1. Does the MP reconstruction for this character fit with the a priori assumptions regarding its evolution when considered ordered?


  12. If we’d define character 11 as an ordered character, would that have any influence on the shape of the tree?


  13. Consider character 2. At some nodes the ancestral states can not be inferred. Why is that? How is this called in MacClade?


  14. Many of the Lemurs are sympatric and quite closely related. Do you think (dis-) similarities in communication signals (like mating calls) are good indicators for relatedness in this situation? Why (not)?


  15. Go back to PAUP. Delete the taxa E. coronatus, E. fulvus, H. aureus, H. simus and I. indri from the matrix. Run a bootstrap analysis and print the resulting (rooted!) tree (use the 'Print Bootstrap Consensus' command or you won't print the bootstrap values - oh, and use 'rectangular' rather than 'slanted': it's probably easier to interpret (well, at least, I think so)). We're going to call this tree "A". Write on every tree you print what search method and what data set was used to construct the tree. We’re going to compare this tree to trees we’re going to construct using molecular data.

    Name:

    Student #:

    E-Mail address: